Taking sequence to bedside is the stated and primary focus of the NHGRI for the next 5 years. Ironically, cheap genome sequencing is now producing analysis bottlenecks, especially as regards the clinical interpretation of genetic variants. The purpose of this SBIR FastTrack proposal is to obtain funding for the integration of two innovative analysis tools, developed by the PIs in parts by other NIH sponsored projects, to produce an integrated system called CGIS for sequenced-based clinical diagnostics using personal genome sequences. CGIS will greatly speed the clinical decision making process, and hence has enormous potential for commercial impact. Early adopters and collaborators include ARUP, one of the nation's top tier diagnostic, CLIA regulated, reference laboratories.